微阵列比较基因组杂交技术与二代基因测序检测拷贝数变异的对比  

The comparison between array-CGH with next generation sequencing in the detection of copy number variations

作　　者：陈新周 王明珠[2] 何丹 周慧 林方欣 李粉霞[2] 

机构地区：[1]广州市达瑞生物技术股份有限公司,广东广州510665 [2]南方医科大学检验与生物技术学院,广东广州510515

出　　处：《分子诊断与治疗杂志》2016年第6期385-388,共4页Journal of Molecular Diagnostics and Therapy

基　　金：广州市科技计划产学研协同创新重大专项(201604020104);广东省科技计划项目公益研究与能力建设专项(2015A030401040);广州市重大科技攻关项目子课题(2014Y2-00220)

摘　　要：目的对比分析微阵列比较基因组杂交技术(array-based comparative genomic hybridization,aCGH)和第二代基因测序技术(next generation sequencing,NGS)在基因组拷贝数变异(copy number variation,CNV)上的一致性,为临床检测CNV提供新的检测方法。方法提取15例流产组织临床样本的基因组DNA,然后分别使用aCGH和NGS 2种方法对上述DNA进行检测,分析对比每个样本的CNV的数目。结果 aCGH共检测到CNV数有109个,最小的片段有16 kb,最大的片段有34 Mb,其中小于200 kb的有20个,大于200 kb小于1 Mb的有34个,大于1 Mb小于5 Mb的有26个,大于5 Mb小于34 Mb的有29个。NGS共检出68个CNV,其中小于200 kb的有3个,检出率为15.0%;大于200 kb小于1 Mb的有22个,检出率为64.7%;大于1 Mb小于5 Mb的有20个,检出率为76.9%;大于5 Mb小于34 Mb的有29个,检出率为100.0%。结论对于目前的数据量来说,NGS在检测大于5 Mb的大片段CNV上检出率较高,与aCGH具有一定的一致性,可以应用于流产组织中CNV的检测。对于小片段的CNV的检测,需要增加相应的读取的数据量进行检测。Objective To provide a new method for clinical detection of copy number variants（CNV） by comparing the consistency between array-based comparative genomic hybridization（a CGH） and next generation sequencing（NGS） in the genome copy number variation. Methods DNA was extracted from 15 cases of clinical specimens and detected by both a CGH and NGS methods. CNV numbers were analyzed in each sample. Results The results showed that a CGH identified 109 CNVs, in that the shortest CNV was 16 KB, and the longest CNV was 34 MB. There were 20 CNVs shorter than 200 kb, 34 CNVs between 200 kb and1 Mb, 26 CNVs between 1 Mb and 5 Mb, and 29 CNVs between 5 Mb and 34 Mb. NGS identified 68 CNVs, of them 3 were shorter than 200 kb（15%）, 22 between 200 kb and 1 Mb（64.7%）, 20 between 1 Mb and 5 Mb（76.9%）, 29 between 5 Mb and 34 Mb（100%）. Conclusion NGS has good consistency with a CGH in detecting CNVs longer than 5 Mb. Therefor it can be a reliable method to test the CNV. The performance of NGS in testing the short CNVs, especially the CNVs shorter than 200 kb will have a better result by increasing the read data.

关 键 词：基因组拷贝数变异 第二代基因测序 微阵列比较基因组杂交技术 

分 类 号：R440[医药卫生—诊断学] R714.21[医药卫生—临床医学]